def test_reasons():
"""Test the reasons class, which is basically a dictionary with a nice
printed output"""
reasons = Reasons()
reasons.add_reason("test reason", 100)
assert reasons.reasons["test reason"] == 100
print(reasons)
expected_output = """Reflections passing individual criteria:
criterion: test reason, reflections: 100
"""
assert reasons.__repr__() == expected_output
def calculate_scaling_subset_ranges_with_E2(reflection_table, params):
"""Select reflections with non-zero weight and update scale weights."""
reasons = Reasons()
selection = ~reflection_table.get_flags(
reflection_table.flags.user_excluded_in_scaling)
selection &= ~reflection_table.get_flags(
reflection_table.flags.excluded_for_scaling)
reasons.add_reason("suitable/selected for scaling", selection.count(True))
if reflection_table["Esq"].count(1.0) != reflection_table.size():
sel, reason = _determine_E2_range_selection(reflection_table, params)
reasons.add_reason(reason, sel.count(True))
selection &= sel
sel, reasons = _common_range_selections(reasons, reflection_table, params)
selection &= sel
logger.info(
"%s reflections were selected for scale factor determination \n" +
"out of %s suitable reflections: \n%s",
selection.count(True),
reflection_table.size(),
reasons,
)
if selection.count(True) == 0:
raise BadDatasetForScalingException(
"""No reflections pass all user-controllable selection criteria""")
return selection
def filter_bad_reflections(cls, reflections):
"""Initial filter to select integrated reflections."""
reasons = Reasons()
mask = ~reflections.get_flags(reflections.flags.integrated, all=False)
reasons.add_reason("not integrated by any method", mask.count(True))
if "d" in reflections:
d_mask = reflections["d"] <= 0.0
reasons.add_reason("bad d-value", d_mask.count(True))
mask = mask | d_mask
reflections.set_flags(mask, reflections.flags.excluded_for_scaling)
return reflections, reasons
def calculate_scaling_subset_ranges(reflection_table,
params,
print_summary=False):
selection, reasons = _common_range_selections(Reasons(), reflection_table,
params)
if print_summary:
logger.info(
"%s reflections were preselected for scale factor determination \n"
+ "out of %s suitable reflections: \n%s",
selection.count(True),
reflection_table.size(),
reasons,
)
if selection.count(True) == 0:
raise BadDatasetForScalingException(
"""No reflections pass all user-controllable selection criteria""")
return selection
def create(cls, params, experiment, reflection_table, for_multi=False):
"""Perform reflection_table preprocessing and create a SingleScaler."""
cls.ensure_experiment_identifier(experiment, reflection_table)
logger.info(
"The scaling model type being applied is %s. \n",
experiment.scaling_model.id_,
)
try:
reflection_table = cls.filter_bad_reflections(
reflection_table,
partiality_cutoff=params.cut_data.partiality_cutoff,
min_isigi=params.cut_data.min_isigi,
)
except ValueError:
raise BadDatasetForScalingException
if "inverse_scale_factor" not in reflection_table:
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
elif (reflection_table["inverse_scale_factor"].count(0.0) ==
reflection_table.size()):
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
reflection_table = choose_scaling_intensities(
reflection_table, params.reflection_selection.intensity_choice)
excluded_for_scaling = reflection_table.get_flags(
reflection_table.flags.excluded_for_scaling)
user_excluded = reflection_table.get_flags(
reflection_table.flags.user_excluded_in_scaling)
reasons = Reasons()
reasons.add_reason("user excluded", user_excluded.count(True))
reasons.add_reason("excluded for scaling",
excluded_for_scaling.count(True))
n_excluded = (excluded_for_scaling | user_excluded).count(True)
if n_excluded == reflection_table.size():
logger.info(
"All reflections were determined to be unsuitable for scaling."
)
logger.info(reasons)
raise BadDatasetForScalingException(
"""Unable to use this dataset for scaling""")
else:
logger.info(
"Excluding %s/%s reflections\n%s",
n_excluded,
reflection_table.size(),
reasons,
)
if params.reflection_selection.method == "intensity_ranges":
reflection_table = quasi_normalisation(reflection_table,
experiment)
if (params.reflection_selection.method
in (None, Auto, "auto", "quasi_random")) or (
experiment.scaling_model.id_ == "physical"
and "absorption" in experiment.scaling_model.components):
if experiment.scan:
# calc theta and phi cryst
reflection_table["phi"] = (
reflection_table["xyzobs.px.value"].parts()[2] *
experiment.scan.get_oscillation()[1])
reflection_table = calc_crystal_frame_vectors(
reflection_table, experiment)
return SingleScaler(params, experiment, reflection_table, for_multi)
def create(cls, params, experiment, reflection_table, for_multi=False):
"""Perform reflection_table preprocessing and create a SingleScaler."""
cls.ensure_experiment_identifier(experiment, reflection_table)
logger.info(
"The scaling model type being applied is %s. \n",
experiment.scaling_model.id_,
)
try:
reflection_table = cls.filter_bad_reflections(
reflection_table,
partiality_cutoff=params.cut_data.partiality_cutoff,
min_isigi=params.cut_data.min_isigi,
intensity_choice=params.reflection_selection.intensity_choice,
)
except ValueError:
raise BadDatasetForScalingException
# combine partial measurements of same reflection, to handle those reflections
# that were split by dials.integrate - changes size of reflection table.
reflection_table = sum_partial_reflections(reflection_table)
if "inverse_scale_factor" not in reflection_table:
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
elif (reflection_table["inverse_scale_factor"].count(0.0) ==
reflection_table.size()):
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
reflection_table = choose_initial_scaling_intensities(
reflection_table, params.reflection_selection.intensity_choice)
excluded_for_scaling = reflection_table.get_flags(
reflection_table.flags.excluded_for_scaling)
user_excluded = reflection_table.get_flags(
reflection_table.flags.user_excluded_in_scaling)
reasons = Reasons()
reasons.add_reason("user excluded", user_excluded.count(True))
reasons.add_reason("excluded for scaling",
excluded_for_scaling.count(True))
n_excluded = (excluded_for_scaling | user_excluded).count(True)
if n_excluded == reflection_table.size():
logger.info(
"All reflections were determined to be unsuitable for scaling."
)
logger.info(reasons)
raise BadDatasetForScalingException(
"""Unable to use this dataset for scaling""")
else:
logger.info(
"Excluding %s/%s reflections\n%s",
n_excluded,
reflection_table.size(),
reasons,
)
if params.reflection_selection.method == "intensity_ranges":
reflection_table = quasi_normalisation(reflection_table,
experiment)
if (params.reflection_selection.method
in (None, Auto, "auto", "quasi_random")) or (
experiment.scaling_model.id_ == "physical"
and "absorption" in experiment.scaling_model.components):
if experiment.scan:
reflection_table = calc_crystal_frame_vectors(
reflection_table, experiment)
alignment_axis = (1.0, 0.0, 0.0)
reflection_table["s0c"] = align_axis_along_z(
alignment_axis, reflection_table["s0c"])
reflection_table["s1c"] = align_axis_along_z(
alignment_axis, reflection_table["s1c"])
try:
scaler = SingleScaler(params, experiment, reflection_table,
for_multi)
except BadDatasetForScalingException as e:
raise ValueError(e)
else:
return scaler
